Align BadK (characterized)
to candidate WP_057507562.1 ABB28_RS04910 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_001431535.1:WP_057507562.1 Length = 265 Score = 118 bits (296), Expect = 1e-31 Identities = 86/246 (34%), Positives = 120/246 (48%), Gaps = 3/246 (1%) Query: 9 ETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGN-TRAFAAGADI 67 E G V +ITL+ P +L AL + A +AD I A+VI+G + F+AGAD+ Sbjct: 15 EADGHVAVITLHNPPAHTWTVHSLA-ALRDLVAALNADRSIYALVISGEGEKFFSAGADL 73 Query: 68 ASMAAWSYSDVY-GSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSA 126 A+ + +E + R +AA+ G A GGG E ALACD+ I A Sbjct: 74 NQFASGDRGAAREAARRFGEAFEALSGFRGVSIAAINGYAMGGGLECALACDLRIIEEHA 133 Query: 127 KFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRL 186 + ALPE +GLLP AGGTQ LPR +G+ A M L ++A+ A R GL + Sbjct: 134 QVALPEATVGLLPCAGGTQNLPRLVGEGWAKRMILLGERIDADTAVRIGLAEQKAGKGEA 193 Query: 187 RDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQA 246 + + A S ++ A K + T A ++ ER F SAD EG+ A Sbjct: 194 KALALEWAKKAGKQSPTSIAACKTLVQSTRTGTHAAALVAEREAFVDLFDSADQVEGVSA 253 Query: 247 FLEKRA 252 FLEKR+ Sbjct: 254 FLEKRS 259 Lambda K H 0.321 0.135 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 140 Number of extensions: 6 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 258 Length of database: 265 Length adjustment: 25 Effective length of query: 233 Effective length of database: 240 Effective search space: 55920 Effective search space used: 55920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory